Data Scales¶
Scales (or “transformations”) are commonly used to improve visualization of cytometry data. Scales are only used for gating and for displaying dot plots and histograms; statistics are calculated on raw, compensated data.
Minimum and Maximum Values¶
All scales have minimum and maximum values. Data points outside of this range are shown as a pile-up on the axes. Gates that include the minimum or maximum scale value will include all datapoints below or above the minimum or maximum, respectively.
Scale Types¶
Linear¶
Linear scales do not affect the data, except that data is clamped within the minimum and maximum values as described above.
Log¶
Log scales apply the common logarithm function (log10). They are sometimes used for scatter parameters, but are less commonly used for fluorescent parameters because they cannot display values less than or equal to zero.
ArcSinh (inverse hyperbolic sine)¶
A limitation of the log scale is the inability to show values at or below zero. The arcsinh function is log-like, but is able to show zero and negative values.
The cofactor parameter adjusts “compression” around zero by dividing the input by this value.
The explicit formula is \(ArcSinh(\frac{x}{c})\). This scale type is generally interchangeable with “biexponential” or “logicle” scales.
Biexponential Scales
CellEngine does not support biexponential scales. ArcSinh is very similar to biexponential, while also being more intuitive and widely used across bioscience fields (e.g., genomics).
Adjusting Scales¶
When uploading FCS files, CellEngine applies instrument-specific defaults. Subsequently, you can manually or automatically adjust the scales to better suit the data.
Howto
- From the gating page, click Edit Scales. A dialog will open.
- To manually change scales: Select the channel to adjust by either clicking into the channel's row, or selecting the X channel on the preview plot. As desired, select the scale type, minimum, maximum and/or cofactor.
- To automatically change scales, do one of the following. Note that this feature only works for arcsinh scales.
- Select one or more rows, then click Autoscale Selected.
- Right-click on a row or click its three-dot menu, then click Autoscale.
Changing Scales after Gating
If you change a scale type or arcsinh cofactor after gating, CellEngine will re-fit the gate coordinates to the new scale. However, because log and arcsinh are non-linear functions, gate edges that were straight with one scale may be curved with another scale. CellEngine does not use curved gate edges; thus, the adjusted gate is only approximately positioned. Depending on the magnitude of the scale change, your gates may require adjustments after changing a scale.
Importing Scales from Other Experiments¶
You can import scales from another experiment from the gating page.